There are currently a number of different methods used to identify viruses. These generally can be classified as either of three types: "rapid diagnosis," genome identification and routine virus diagnosis.
Rapid diagnosis methods are based on antigen-antibody systems which are specific for particular viruses. These antibodies may be polyclonal or monoclonal. Typically these systems utilize visual signals such as color changes to signify a match between the antibody and the associated virus. While many of these antibody probes are available commercially, virus identification by their use suffers from a number of drawbacks. For one, the commercial probes which are available vary widely in quality, specificity and sensitivity. More importantly, however, the utility of these probes requires a significant degree of virus identification by the analyst prior to use of the probe. Because each probe is specific to one virus or a small group of related viruses, the analyst must have a good idea of which virus is involved in order to determine which type of probe is most likely to be effective. The choice of probes must be narrowed as much as possible for both practical and economic reasons. Conversely, where the general type of virus cannot be preliminarily identified, identification becomes very time-consuming and costly because of the need to work through a series of probes before the virus can be identified.
Another general category of prior art processes is genome identification. This requires specifically prepared probes of highly conserved genomic regions and use of these probes in hydridization procedures. Complete mapping requires libraries of individual probes and preparation of specially radiolabeled nucleic acid fragments. Specially equipped laboratories are the only ones who can perform such identification and the skills of specially trained analysts are necessary. Thus the technique, while effective, is costly, labor intensive and not practical for many routine identification requirements.
A third technique used is designated "routine virus diagnosis" and is based on clinical and laboratory virology. By using a number of related and sequential techniques of tissue culture and other analyses, virus identification can be accomplished. However, the techniques needed are complex and require specialized tissue cultures, analysis materials and equipment, such that the methods can be practiced by only a small number of specialized laboratories, such as those found in government agencies or universities. Further, the completion of a diagnostic report generally takes a matter of several days to many weeks, thus making the technique impractival for medical diagnosis and treatment where prompt identification of a virus is critical. Further, even many of the laboratories equipped for this type of diagnosis do not have the capability of further characterizing these isolated viruses.
There have in the past been automated techniques for identifying bacteria for electrophoresis methods, including sodium dodecyl sulfate polyacrylamide gel electrophoresis ("SDS-PAGE"). Two reports of particular interest are Hook et al. Devel. Ind. Microbiol., 28, 149 (1987) [J. Ind. Microbiol. Suppl. 2] and Silman, U.S. Pat. No. 4,521,512. Both Hook et al. and Silman disclose a number of strains of bacteria which can be identified by obtaining an electrophoresis analysis and comparing the analysis with a library of like analyses for previously identified bacteria. The techniques described work quite well for bacterial analysis, since bacterial protein analysis is unaffected by the presence of host cell proteins. In addition, bacteria are relatively complex organisms and are able to grow in synthetic media outside the cell. Upon routine electrophoretic separation, they produce many protein bands which are microbe specific and thus can be readily identified using simple pattern recognition software. Viruses, on the other hand, require live cell systems for growth. When viral cultures are subjected to SDS-PAGE, very few viral protein bands are seen among hundreds of bands for cell specific proteins.
The Silman patent suggests that its disclosed method could be applicable to the identification of "viruses or other microorganisms which require a host cell for metabolic activity." However, it can be shown that the Silman technique is applicable only to those few viruses which spontaneously and consistently suppress the synthesis of proteins of host cells in which they replicate. The viruses of consequence among these few are the herpes simplex viruses, HSV-1 and HSV-2, which are also the only viruses mentioned by Silman. Consequently, with this exception, the Silman method is applicable only to microbes which grow in synthetic media. For most viruses, the continued production of proteins by the host cell effectively precludes any consistent and accurate virus identification by known electrophoretic techniques.
It would therefore be of great value to have a virus identification technique which could be performed relatively rapidly using well-known readily available analysis methods and which would be capable of being performed on a routine basis by a wide number of analytical laboratories or even by individual researchers. Further, it would be advantageous to have a technique which would permit the immediate screening and identification of a wide variety of related and unrelated viruses with a single procedure, so that an analyst could identify a virus even with little or no preidentification of the virus. It would also be advantageous to have an identification procedure which could be used in a conventional virology laboratory.